def test_queryengine_io(self, fn):
skip_if_no_external('h5py')
from mvpa2.base.hdf5 import h5save, h5load
vol_shape = (10, 10, 10, 1)
vol_affine = np.identity(4)
vg = volgeom.VolGeom(vol_shape, vol_affine)
# generate some surfaces,
# and add some noise to them
sphere_density = 10
outer = surf.generate_sphere(sphere_density) * 5 + 8
inner = surf.generate_sphere(sphere_density) * 3 + 8
radius = 5.
add_fa = ['center_distances', 'grey_matter_position']
qe = disc_surface_queryengine(radius, vg, inner, outer, add_fa=add_fa)
ds = fmri_dataset(vg.get_masked_nifti_image())
# the following is not really a strong requirement. XXX remove?
assert_raises(ValueError, lambda: qe[qe.ids[0]])
# check that after training it behaves well
qe.train(ds)
i = qe.ids[0]
try:
m = qe[i]
except ValueError, e:
raise AssertionError(
'Failed to query %r from %r after training on %r. Exception was: %r'
% (i, qe, ds, e))
def test_queryengine_io(self, fn):
skip_if_no_external("h5py")
from mvpa2.base.hdf5 import h5save, h5load
vol_shape = (10, 10, 10, 1)
vol_affine = np.identity(4)
vg = volgeom.VolGeom(vol_shape, vol_affine)
# generate some surfaces,
# and add some noise to them
sphere_density = 10
outer = surf.generate_sphere(sphere_density) * 5 + 8
inner = surf.generate_sphere(sphere_density) * 3 + 8
radius = 5.0
add_fa = ["center_distances", "grey_matter_position"]
qe = disc_surface_queryengine(radius, vg, inner, outer, add_fa=add_fa)
ds = fmri_dataset(vg.get_masked_nifti_image())
# the following is not really a strong requirement. XXX remove?
assert_raises(ValueError, lambda: qe[qe.ids[0]])
# check that after training it behaves well
qe.train(ds)
i = qe.ids[0]
try:
m = qe[i]
except ValueError, e:
raise AssertionError(
"Failed to query %r from %r after training on %r. " "Exception was: %r" % (i, qe, ds, e)
)
def test_h5support(self):
sh = (20, 20, 20)
msk = np.zeros(sh)
for i in xrange(0, sh[0], 2):
msk[i, :, :] = 1
vg = volgeom.VolGeom(sh, np.identity(4), mask=msk)
density = 20
outer = surf.generate_sphere(density) * 10. + 5
inner = surf.generate_sphere(density) * 5. + 5
intermediate = outer * .5 + inner * .5
xyz = intermediate.vertices
radius = 50
backends = ['native', 'hdf5']
for i, backend in enumerate(backends):
if backend == 'hdf5' and not externals.exists('h5py'):
continue
sel = surf_voxel_selection.run_voxel_selection(radius, vg, inner,
outer, results_backend=backend)
if i == 0:
sel0 = sel
else:
assert_equal(sel0, sel)
def test_surface_voxel_query_engine(self):
vol_shape = (10, 10, 10, 1)
vol_affine = np.identity(4)
vol_affine[0, 0] = vol_affine[1, 1] = vol_affine[2, 2] = 5
vg = volgeom.VolGeom(vol_shape, vol_affine)
# make the surfaces
sphere_density = 10
outer = surf.generate_sphere(sphere_density) * 25. + 15
inner = surf.generate_sphere(sphere_density) * 20. + 15
vs = volsurf.VolSurfMaximalMapping(vg, inner, outer)
radius = 10
for fallback, expected_nfeatures in ((True, 1000), (False, 183)):
voxsel = surf_voxel_selection.voxel_selection(vs, radius)
qe = SurfaceVoxelsQueryEngine(voxsel,
fallback_euclidian_distance=fallback)
m = _Voxel_Count_Measure()
sl = Searchlight(m, queryengine=qe)
data = np.random.normal(size=vol_shape)
img = nb.Nifti1Image(data, vol_affine)
ds = fmri_dataset(img)
sl_map = sl(ds)
counts = sl_map.samples
assert_true(np.all(np.logical_and(5 <= counts, counts <= 18)))
assert_equal(sl_map.nfeatures, expected_nfeatures)
def test_surface_voxel_query_engine(self):
vol_shape = (10, 10, 10, 1)
vol_affine = np.identity(4)
vol_affine[0, 0] = vol_affine[1, 1] = vol_affine[2, 2] = 5
vg = volgeom.VolGeom(vol_shape, vol_affine)
# make the surfaces
sphere_density = 10
outer = surf.generate_sphere(sphere_density) * 25. + 15
inner = surf.generate_sphere(sphere_density) * 20. + 15
vs = volsurf.VolSurfMaximalMapping(vg, inner, outer)
radius = 10
for fallback, expected_nfeatures in ((True, 1000), (False, 183)):
voxsel = surf_voxel_selection.voxel_selection(vs, radius)
qe = SurfaceVoxelsQueryEngine(voxsel, fallback_euclidian_distance=fallback)
m = _Voxel_Count_Measure()
sl = Searchlight(m, queryengine=qe)
data = np.random.normal(size=vol_shape)
img = nb.Nifti1Image(data, vol_affine)
ds = fmri_dataset(img)
sl_map = sl(ds)
counts = sl_map.samples
assert_true(np.all(np.logical_and(5 <= counts, counts <= 18)))
assert_equal(sl_map.nfeatures, expected_nfeatures)
def test_h5support(self):
sh = (20, 20, 20)
msk = np.zeros(sh)
for i in xrange(0, sh[0], 2):
msk[i, :, :] = 1
vg = volgeom.VolGeom(sh, np.identity(4), mask=msk)
density = 20
outer = surf.generate_sphere(density) * 10. + 5
inner = surf.generate_sphere(density) * 5. + 5
intermediate = outer * .5 + inner * .5
xyz = intermediate.vertices
radius = 50
backends = ['native', 'hdf5']
for i, backend in enumerate(backends):
if backend == 'hdf5' and not externals.exists('h5py'):
continue
sel = surf_voxel_selection.run_voxel_selection(
radius, vg, inner, outer, results_backend=backend)
if i == 0:
sel0 = sel
else:
assert_equal(sel0, sel)
def test_surface_minimal_voxel_selection(self):
# Tests 'minimal' voxel selection.
# It assumes that 'maximal' voxel selection works (which is tested
# in other unit tests)
vol_shape = (10, 10, 10, 1)
vol_affine = np.identity(4)
vg = volgeom.VolGeom(vol_shape, vol_affine)
# generate some surfaces,
# and add some noise to them
sphere_density = 10
nvertices = sphere_density**2 + 2
noise = np.random.uniform(size=(nvertices, 3))
outer = surf.generate_sphere(sphere_density) * 5 + 8 + noise
inner = surf.generate_sphere(sphere_density) * 3 + 8 + noise
radii = [5., 20., 10] # note: no fixed radii at the moment
# Note: a little outside margin is necessary
# as otherwise there are nodes in the minimal case
# that have no voxels associated with them
for radius in radii:
for output_modality in ('surface', 'volume'):
for i, nvm in enumerate(('minimal', 'maximal')):
qe = disc_surface_queryengine(
radius,
vg,
inner,
outer,
node_voxel_mapping=nvm,
output_modality=output_modality)
voxsel = qe.voxsel
if i == 0:
keys_ = voxsel.keys()
voxsel_ = voxsel
else:
keys = voxsel.keys()
# minimal one has a subset
assert_equal(keys, keys_)
# and the subset is quite overlapping
assert_true(len(keys) * .90 < len(keys_))
for k in keys_:
x = set(voxsel_[k])
y = set(voxsel[k])
d = set.symmetric_difference(x, y)
r = float(len(d)) / 2 / len(x)
if type(radius) is float:
assert_equal(x - y, set())
# decent agreement in any case
# between the two sets
assert_true(r < .6)
def test_niml_dset_voxsel(self, fn):
if not externals.exists('nibabel'):
return
# This is actually a bit of an integration test.
# It tests storing and retrieving searchlight results.
# Imports are inline here so that it does not mess up the header
# and makes the other unit tests more modular
# XXX put this in a separate file?
from mvpa2.misc.surfing import volgeom, surf_voxel_selection, queryengine
from mvpa2.measures.searchlight import Searchlight
from mvpa2.support.nibabel import surf
from mvpa2.measures.base import Measure
from mvpa2.datasets.mri import fmri_dataset
class _Voxel_Count_Measure(Measure):
# used to check voxel selection results
is_trained = True
def __init__(self, dtype, **kwargs):
Measure.__init__(self, **kwargs)
self.dtype = dtype
def _call(self, dset):
return self.dtype(dset.nfeatures)
sh = (20, 20, 20)
vg = volgeom.VolGeom(sh, np.identity(4))
density = 20
outer = surf.generate_sphere(density) * 10. + 5
inner = surf.generate_sphere(density) * 5. + 5
intermediate = outer * .5 + inner * .5
xyz = intermediate.vertices
radius = 50
sel = surf_voxel_selection.run_voxel_selection(radius, vg, inner, outer)
qe = queryengine.SurfaceVerticesQueryEngine(sel)
for dtype in (int, float):
sl = Searchlight(_Voxel_Count_Measure(dtype), queryengine=qe)
ds = fmri_dataset(vg.get_empty_nifti_image(1))
r = sl(ds)
niml.write(fn, r)
rr = niml.read(fn)
os.remove(fn)
assert_array_equal(r.samples, rr.samples)
def test_niml_dset_voxsel(self):
if not externals.exists('nibabel'):
return
# This is actually a bit of an integration test.
# It tests storing and retrieving searchlight results.
# Imports are inline here so that it does not mess up the header
# and makes the other unit tests more modular
# XXX put this in a separate file?
from mvpa2.misc.surfing import volgeom, surf_voxel_selection, queryengine
from mvpa2.measures.searchlight import Searchlight
from mvpa2.support.nibabel import surf
from mvpa2.measures.base import Measure
from mvpa2.datasets.mri import fmri_dataset
class _Voxel_Count_Measure(Measure):
# used to check voxel selection results
is_trained = True
def __init__(self, dtype, **kwargs):
Measure.__init__(self, **kwargs)
self.dtype = dtype
def _call(self, dset):
return self.dtype(dset.nfeatures)
sh = (20, 20, 20)
vg = volgeom.VolGeom(sh, np.identity(4))
density = 20
outer = surf.generate_sphere(density) * 10. + 5
inner = surf.generate_sphere(density) * 5. + 5
intermediate = outer * .5 + inner * .5
xyz = intermediate.vertices
radius = 50
sel = surf_voxel_selection.run_voxel_selection(radius, vg, inner,
outer)
qe = queryengine.SurfaceVerticesQueryEngine(sel)
for dtype in (int, float):
sl = Searchlight(_Voxel_Count_Measure(dtype), queryengine=qe)
ds = fmri_dataset(vg.get_empty_nifti_image(1))
r = sl(ds)
_, fn = tempfile.mkstemp('.niml.dset', 'dset')
niml_dset.write(fn, r)
rr = niml_dset.read(fn)
os.remove(fn)
assert_array_equal(r.samples, rr.samples)
def test_surface_minimal_voxel_selection(self):
# Tests 'minimal' voxel selection.
# It assumes that 'maximal' voxel selection works (which is tested
# in other unit tests)
vol_shape = (10, 10, 10, 1)
vol_affine = np.identity(4)
vg = volgeom.VolGeom(vol_shape, vol_affine)
# generate some surfaces,
# and add some noise to them
sphere_density = 10
nvertices = sphere_density ** 2 + 2
noise = np.random.uniform(size=(nvertices, 3))
outer = surf.generate_sphere(sphere_density) * 5 + 8 + noise
inner = surf.generate_sphere(sphere_density) * 3 + 8 + noise
radii = [5.0, 20.0, 10] # note: no fixed radii at the moment
# Note: a little outside margin is necessary
# as otherwise there are nodes in the minimal case
# that have no voxels associated with them
for radius in radii:
for output_modality in ("surface", "volume"):
for i, nvm in enumerate(("minimal", "maximal")):
qe = disc_surface_queryengine(
radius, vg, inner, outer, node_voxel_mapping=nvm, output_modality=output_modality
)
voxsel = qe.voxsel
if i == 0:
keys_ = voxsel.keys()
voxsel_ = voxsel
else:
keys = voxsel.keys()
# minimal one has a subset
assert_equal(keys, keys_)
# and the subset is quite overlapping
assert_true(len(keys) * 0.90 < len(keys_))
for k in keys_:
x = set(voxsel_[k])
y = set(voxsel[k])
d = set.symmetric_difference(x, y)
r = float(len(d)) / 2 / len(x)
if type(radius) is float:
assert_equal(x - y, set())
# decent agreement in any case
# between the two sets
assert_true(r < 0.6)
def test_surface_outside_volume_voxel_selection(self, fn):
skip_if_no_external('h5py')
from mvpa2.base.hdf5 import h5save, h5load
vol_shape = (10, 10, 10, 1)
vol_affine = np.identity(4)
vg = volgeom.VolGeom(vol_shape, vol_affine)
# make surfaces that are far away from all voxels
# in the volume
sphere_density = 4
far = 10000.
outer = surf.generate_sphere(sphere_density) * 10 + far
inner = surf.generate_sphere(sphere_density) * 5 + far
vs = volsurf.VolSurfMaximalMapping(vg, inner, outer)
radii = [10., 10] # fixed and variable radii
outside_node_margins = [0, far, True]
for outside_node_margin in outside_node_margins:
for radius in radii:
selector = lambda: surf_voxel_selection.voxel_selection(vs,
radius,
outside_node_margin=outside_node_margin)
if type(radius) is int and outside_node_margin is True:
assert_raises(ValueError, selector)
else:
sel = selector()
if outside_node_margin is True:
# it should have all the keys, but they should
# all be empty
assert_array_equal(sel.keys(), range(inner.nvertices))
for k, v in sel.iteritems():
assert_equal(v, [])
else:
assert_array_equal(sel.keys(), [])
if outside_node_margin is True and \
externals.versions['hdf5'] < '1.8.7':
raise SkipTest("Versions of hdf5 before 1.8.7 have "
"problems with empty arrays")
h5save(fn, sel)
sel_copy = h5load(fn)
assert_array_equal(sel.keys(), sel_copy.keys())
for k in sel.keys():
assert_equal(sel[k], sel_copy[k])
assert_equal(sel, sel_copy)
def test_surface_outside_volume_voxel_selection(self, fn):
skip_if_no_external('h5py')
from mvpa2.base.hdf5 import h5save, h5load
vol_shape = (10, 10, 10, 1)
vol_affine = np.identity(4)
vg = volgeom.VolGeom(vol_shape, vol_affine)
# make surfaces that are far away from all voxels
# in the volume
sphere_density = 4
far = 10000.
outer = surf.generate_sphere(sphere_density) * 10 + far
inner = surf.generate_sphere(sphere_density) * 5 + far
vs = volsurf.VolSurfMaximalMapping(vg, inner, outer)
radii = [10., 10] # fixed and variable radii
outside_node_margins = [0, far, True]
for outside_node_margin in outside_node_margins:
for radius in radii:
selector = lambda: surf_voxel_selection.voxel_selection(vs,
radius,
outside_node_margin=outside_node_margin)
if type(radius) is int and outside_node_margin is True:
assert_raises(ValueError, selector)
else:
sel = selector()
if outside_node_margin is True:
# it should have all the keys, but they should
# all be empty
assert_array_equal(sel.keys(), range(inner.nvertices))
for k, v in sel.iteritems():
assert_equal(v, [])
else:
assert_array_equal(sel.keys(), [])
if outside_node_margin is True and \
externals.versions['hdf5'] < '1.8.7':
raise SkipTest("Versions of hdf5 before 1.8.7 have "
"problems with empty arrays")
h5save(fn, sel)
sel_copy = h5load(fn)
assert_array_equal(sel.keys(), sel_copy.keys())
for k in sel.keys():
assert_equal(sel[k], sel_copy[k])
assert_equal(sel, sel_copy)
def test_volsurf(self):
vg = volgeom.VolGeom((50, 50, 50), np.identity(4))
density = 40
outer = surf.generate_sphere(density) * 25. + 25
inner = surf.generate_sphere(density) * 20. + 25
# increasingly select more voxels in 'grey matter'
steps_start_stop = [(1, .5, .5), (5, .5, .5), (3, .3, .7), (5, .3, .7),
(5, 0., 1.), (10, 0., 1.)]
mp = None
expected_keys = set(range(density**2 + 2))
selection_counter = []
voxel_counter = []
for sp, sa, so in steps_start_stop:
vs = volsurf.VolSurfMaximalMapping(vg, outer, inner,
(outer + inner) * .5, sp, sa,
so)
n2v = vs.get_node2voxels_mapping()
if mp is None:
mp = n2v
assert_equal(expected_keys, set(n2v.keys()))
counter = 0
for k, v2pos in n2v.iteritems():
for v, pos in v2pos.iteritems():
# should be close to grey matter
assert_true(-1. <= pos <= 2.)
counter += 1
selection_counter.append(counter)
img = vs.voxel_count_nifti_image()
voxel_counter.append(np.sum(img.get_data() > 0))
# hard coded number of expected voxels
selection_expected = [1602, 1602, 4618, 5298, 7867, 10801]
assert_equal(selection_counter, selection_expected)
voxel_expected = [1498, 1498, 4322, 4986, 7391, 10141]
assert_equal(voxel_counter, voxel_expected)
# check that string building works
assert_true(len('%s%r' % (vs, vs)) > 0)
def test_volsurf(self):
vg = volgeom.VolGeom((50, 50, 50), np.identity(4))
density = 40
outer = surf.generate_sphere(density) * 25. + 25
inner = surf.generate_sphere(density) * 20. + 25
# increasingly select more voxels in 'grey matter'
steps_start_stop = [(1, .5, .5), (5, .5, .5), (3, .3, .7),
(5, .3, .7), (5, 0., 1.), (10, 0., 1.)]
mp = None
expected_keys = set(range(density ** 2 + 2))
selection_counter = []
voxel_counter = []
for sp, sa, so in steps_start_stop:
vs = volsurf.VolSurfMaximalMapping(vg, outer, inner, (outer + inner) * .5, sp, sa, so)
n2v = vs.get_node2voxels_mapping()
if mp is None:
mp = n2v
assert_equal(expected_keys, set(n2v.keys()))
counter = 0
for k, v2pos in n2v.iteritems():
for v, pos in v2pos.iteritems():
# should be close to grey matter
assert_true(-1. <= pos and pos <= 2.)
counter += 1
selection_counter.append(counter)
img = vs.voxel_count_nifti_image()
voxel_counter.append(np.sum(img.get_data() > 0))
# hard coded number of expected voxels
selection_expected = [1602, 1602, 4618, 5298, 7867, 10801]
assert_equal(selection_counter, selection_expected)
voxel_expected = [1498, 1498, 4322, 4986, 7391, 10141]
assert_equal(voxel_counter, voxel_expected)
# check that string building works
assert_true(len('%s%r' % (vs, vs)) > 0)
def test_surf_fs_asc(self, temp_fn):
s = surf.generate_sphere(5) * 100
surf_fs_asc.write(temp_fn, s, overwrite=True)
t = surf_fs_asc.read(temp_fn)
assert_array_almost_equal(s.vertices, t.vertices)
assert_array_almost_equal(s.vertices, t.vertices)
theta = np.asarray([0, 0., 180.])
r = s.rotate(theta, unit='deg')
l2r = surf.get_sphere_left_right_mapping(s, r)
l2r_expected = [
0, 1, 2, 6, 5, 4, 3, 11, 10, 9, 8, 7, 15, 14, 13, 12, 16, 19, 18,
17, 21, 20, 23, 22, 26, 25, 24
]
assert_array_equal(l2r, np.asarray(l2r_expected))
sides_facing = 'apism'
for side_facing in sides_facing:
l, r = surf.reposition_hemisphere_pairs(s + 10., t + (-10.),
side_facing)
m = surf.merge(l, r)
# not sure at the moment why medial rotation
# messes up - but leave for now
eps = 666 if side_facing == 'm' else .001
assert_true((abs(m.center_of_mass) < eps).all())
def test_surf_fs_asc(self, temp_fn):
s = surf.generate_sphere(5) * 100
surf_fs_asc.write(temp_fn, s, overwrite=True)
t = surf_fs_asc.read(temp_fn)
assert_array_almost_equal(s.vertices, t.vertices)
assert_array_almost_equal(s.vertices, t.vertices)
theta = np.asarray([0, 0., 180.])
r = s.rotate(theta, unit='deg')
l2r = surf.get_sphere_left_right_mapping(s, r)
l2r_expected = [0, 1, 2, 6, 5, 4, 3, 11, 10, 9, 8, 7, 15, 14, 13, 12,
16, 19, 18, 17, 21, 20, 23, 22, 26, 25, 24]
assert_array_equal(l2r, np.asarray(l2r_expected))
sides_facing = 'apism'
for side_facing in sides_facing:
l, r = surf.reposition_hemisphere_pairs(s + 10., t + (-10.),
side_facing)
m = surf.merge(l, r)
# not sure at the moment why medial rotation
# messes up - but leave for now
eps = 666 if side_facing == 'm' else .001
assert_true((abs(m.center_of_mass) < eps).all())
def test_surface_voxel_query_engine(self):
vol_shape = (10, 10, 10, 1)
vol_affine = np.identity(4)
vol_affine[0, 0] = vol_affine[1, 1] = vol_affine[2, 2] = 5
vg = volgeom.VolGeom(vol_shape, vol_affine)
# make the surfaces
sphere_density = 10
outer = surf.generate_sphere(sphere_density) * 25. + 15
inner = surf.generate_sphere(sphere_density) * 20. + 15
vs = volsurf.VolSurfMaximalMapping(vg, inner, outer)
radius = 10
for fallback, expected_nfeatures in ((True, 1000), (False, 183)):
voxsel = surf_voxel_selection.voxel_selection(vs, radius)
qe = SurfaceVoxelsQueryEngine(voxsel,
fallback_euclidean_distance=fallback)
# test i/o and ensure that the loaded instance is trained
if externals.exists('h5py'):
fd, qefn = tempfile.mkstemp('qe.hdf5', 'test');
os.close(fd)
h5save(qefn, qe)
qe = h5load(qefn)
os.remove(qefn)
m = _Voxel_Count_Measure()
sl = Searchlight(m, queryengine=qe)
data = np.random.normal(size=vol_shape)
img = nb.Nifti1Image(data, vol_affine)
ds = fmri_dataset(img)
sl_map = sl(ds)
counts = sl_map.samples
assert_true(np.all(np.logical_and(5 <= counts, counts <= 18)))
assert_equal(sl_map.nfeatures, expected_nfeatures)
def test_surface_voxel_query_engine(self):
vol_shape = (10, 10, 10, 1)
vol_affine = np.identity(4)
vol_affine[0, 0] = vol_affine[1, 1] = vol_affine[2, 2] = 5
vg = volgeom.VolGeom(vol_shape, vol_affine)
# make the surfaces
sphere_density = 10
outer = surf.generate_sphere(sphere_density) * 25. + 15
inner = surf.generate_sphere(sphere_density) * 20. + 15
vs = volsurf.VolSurfMaximalMapping(vg, inner, outer)
radius = 10
for fallback, expected_nfeatures in ((True, 1000), (False, 183)):
voxsel = surf_voxel_selection.voxel_selection(vs, radius)
qe = SurfaceVoxelsQueryEngine(voxsel,
fallback_euclidean_distance=fallback)
# test i/o and ensure that the loaded instance is trained
if externals.exists('h5py'):
fd, qefn = tempfile.mkstemp('qe.hdf5', 'test')
os.close(fd)
h5save(qefn, qe)
qe = h5load(qefn)
os.remove(qefn)
m = _Voxel_Count_Measure()
sl = Searchlight(m, queryengine=qe)
data = np.random.normal(size=vol_shape)
img = nb.Nifti1Image(data, vol_affine)
ds = fmri_dataset(img)
sl_map = sl(ds)
counts = sl_map.samples
assert_true(np.all(np.logical_and(5 <= counts, counts <= 18)))
assert_equal(sl_map.nfeatures, expected_nfeatures)
def test_minimal_dataset(self):
vol_shape = (10, 10, 10, 3)
vol_affine = np.identity(4)
vg = volgeom.VolGeom(vol_shape, vol_affine)
data = np.random.normal(size=vol_shape)
msk = np.ones(vol_shape[:3])
msk[:, 1:-1:2, :] = 0
ni_data = nb.Nifti1Image(data, vol_affine)
ni_msk = nb.Nifti1Image(msk, vol_affine)
ds = fmri_dataset(ni_data, mask=ni_msk)
sphere_density = 20
outer = surf.generate_sphere(sphere_density) * 10. + 5
inner = surf.generate_sphere(sphere_density) * 7. + 5
radius = 10
sel = surf_voxel_selection.run_voxel_selection(radius, ds,
inner, outer)
sel_fids = set.union(*(set(sel[k]) for k in sel.keys()))
ds_vox = map(tuple, ds.fa.voxel_indices)
vg = sel.volgeom
sel_vox = map(tuple, vg.lin2ijk(np.asarray(list(sel_fids))))
fid_mask = np.asarray([v in sel_vox for v in ds_vox])
assert_array_equal(fid_mask, sel.get_dataset_feature_mask(ds))
# check if it raises errors
ni_neg_msk = nb.Nifti1Image(1 - msk, vol_affine)
neg_ds = fmri_dataset(ni_data, mask=ni_neg_msk) # inverted mask
assert_raises(ValueError, sel.get_dataset_feature_mask, neg_ds)
min_ds = sel.get_minimal_dataset(ds)
assert_array_equal(min_ds.samples, ds[:, fid_mask].samples)
def test_minimal_dataset(self):
vol_shape = (10, 10, 10, 3)
vol_affine = np.identity(4)
vg = volgeom.VolGeom(vol_shape, vol_affine)
data = np.random.normal(size=vol_shape)
msk = np.ones(vol_shape[:3])
msk[:, 1:-1:2, :] = 0
ni_data = nb.Nifti1Image(data, vol_affine)
ni_msk = nb.Nifti1Image(msk, vol_affine)
ds = fmri_dataset(ni_data, mask=ni_msk)
sphere_density = 20
outer = surf.generate_sphere(sphere_density) * 10. + 5
inner = surf.generate_sphere(sphere_density) * 7. + 5
radius = 10
sel = surf_voxel_selection.run_voxel_selection(radius, ds,
inner, outer)
sel_fids = set.union(*(set(sel[k]) for k in sel.keys()))
ds_vox = map(tuple, ds.fa.voxel_indices)
vg = sel.volgeom
sel_vox = map(tuple, vg.lin2ijk(np.asarray(list(sel_fids))))
fid_mask = np.asarray([v in sel_vox for v in ds_vox])
assert_array_equal(fid_mask, sel.get_dataset_feature_mask(ds))
# check if it raises errors
ni_neg_msk = nb.Nifti1Image(1 - msk, vol_affine)
neg_ds = fmri_dataset(ni_data, mask=ni_neg_msk) # inverted mask
assert_raises(ValueError, sel.get_dataset_feature_mask, neg_ds)
min_ds = sel.get_minimal_dataset(ds)
assert_array_equal(min_ds.samples, ds[:, fid_mask].samples)
def test_surf_border(self):
s = surf.generate_sphere(3)
assert_array_equal(s.nodes_on_border(), [False] * 11)
s = surf.generate_plane((0, 0, 0), (0, 1, 0), (1, 0, 0), 10, 10)
b = s.nodes_on_border()
v = s.vertices
vb = reduce(np.logical_or,
[v[:, 0] == 0, v[:, 1] == 0, v[:, 0] == 9, v[:, 1] == 9])
assert_array_equal(b, vb)
assert_true(s.nodes_on_border(0))
def test_surf_border(self):
s = surf.generate_sphere(3)
assert_array_equal(s.nodes_on_border(), [False] * 11)
s = surf.generate_plane((0, 0, 0), (0, 1, 0), (1, 0, 0), 10, 10)
b = s.nodes_on_border()
v = s.vertices
vb = reduce(np.logical_or, [v[:, 0] == 0, v[:, 1] == 0,
v[:, 0] == 9, v[:, 1] == 9])
assert_array_equal(b, vb)
assert_true(s.nodes_on_border(0))
def test_mask_with_keys(self):
vol_shape = (10, 10, 10, 3)
vol_affine = np.identity(4)
vg = volgeom.VolGeom(vol_shape, vol_affine)
data = np.random.normal(size=vol_shape)
msk = np.ones(vol_shape[:3])
msk[:, 1:-1:2, :] = 0
ni_data = nb.Nifti1Image(data, vol_affine)
ni_msk = nb.Nifti1Image(msk, vol_affine)
ds = fmri_dataset(ni_data, mask=ni_msk)
sphere_density = 20
outer = surf.generate_sphere(sphere_density) * 10.0 + 5
inner = surf.generate_sphere(sphere_density) * 7.0 + 5
radius = 10
sel = surf_voxel_selection.run_voxel_selection(radius, ds, inner, outer)
# in the mapping below:
# (tup: None) means that tup as input should raise a KeyError
# (tup: i) with i an int means that tup as input should return i
# elements
qe_ids2nvoxels = {
SurfaceVoxelsQueryEngine: {(1, 2, 3): 13, tuple(np.arange(0, 200, 2)): 82, (601,): None, None: 126},
SurfaceVerticesQueryEngine: {(1, 2, 3): None, (205, 209, 210, 214): 36, None: 126},
}
for constructor, ids2nfeatures in qe_ids2nvoxels.iteritems():
qe = constructor(sel)
qe.train(ds)
img = qe.get_masked_nifti_image()
assert_array_equal(img.get_data(), qe.get_masked_nifti_image(qe.ids).get_data())
img_getter = qe.get_masked_nifti_image
for ids, nfeatures in ids2nfeatures.iteritems():
ids_list = ids if ids is None else list(ids)
if nfeatures is None and ids is not None:
assert_raises(KeyError, img_getter, ids_list)
else:
img = img_getter(ids_list)
nfeatures_found = np.sum(img.get_data())
assert_equal(nfeatures, nfeatures_found)
if constructor is SurfaceVerticesQueryEngine:
expected_image = qe.get_masked_nifti_image(ids_list)
expected_mask = expected_image.get_data()
check_mask_func = lambda x: assert_array_equal(expected_mask, x)
check_image_func = lambda x: check_mask_func(x.get_data()) and assert_array_equal(
x.get_affine(), expected_image.get_affine()
)
check_mask_func(sel.get_mask(ids_list))
check_image_func(sel.get_nifti_image_mask(ids_list))
tups = sel.get_voxel_indices(ids_list)
tups_mask = np.zeros(expected_mask.shape)
for tup in tups:
tups_mask[tup] += 1
assert_array_equal(expected_mask != 0, tups_mask != 0)
def test_surf_voxel_selection(self):
vol_shape = (10, 10, 10)
vol_affine = np.identity(4)
vol_affine[0, 0] = vol_affine[1, 1] = vol_affine[2, 2] = 5
vg = volgeom.VolGeom(vol_shape, vol_affine)
density = 10
outer = surf.generate_sphere(density) * 25. + 15
inner = surf.generate_sphere(density) * 20. + 15
vs = volsurf.VolSurfMaximalMapping(vg, outer, inner)
nv = outer.nvertices
# select under variety of parameters
# parameters are distance metric (dijkstra or euclidean),
# radius, and number of searchlight centers
params = [('d', 1., 10), ('d', 1., 50), ('d', 1., 100), ('d', 2., 100),
('e', 2., 100), ('d', 2., 100), ('d', 20, 100),
('euclidean', 5, None), ('dijkstra', 10, None)]
# function that indicates for which parameters the full test is run
test_full = lambda x: len(x[0]) > 1 or x[2] == 100
expected_labs = ['grey_matter_position', 'center_distances']
voxcount = []
tested_double_features = False
for param in params:
distance_metric, radius, ncenters = param
srcs = range(0, nv, nv // (ncenters or nv))
sel = surf_voxel_selection.voxel_selection(
vs,
radius,
source_surf_nodes=srcs,
distance_metric=distance_metric)
# see how many voxels were selected
vg = sel.volgeom
datalin = np.zeros((vg.nvoxels, 1))
mp = sel
for k, idxs in mp.iteritems():
if idxs is not None:
datalin[idxs] = 1
voxcount.append(np.sum(datalin))
if test_full(param):
assert_equal(np.sum(datalin), np.sum(sel.get_mask()))
assert_true(len('%s%r' % (sel, sel)) > 0)
# see if voxels containing inner and outer
# nodes were selected
for sf in [inner, outer]:
for k, idxs in mp.iteritems():
xyz = np.reshape(sf.vertices[k, :], (1, 3))
linidx = vg.xyz2lin(xyz)
# only required if xyz is actually within the volume
assert_equal(linidx in idxs, vg.contains_lin(linidx))
# check that it has all the attributes
labs = sel.aux_keys()
assert_true(all([lab in labs for lab in expected_labs]))
if externals.exists('h5py'):
# some I/O testing
fd, fn = tempfile.mkstemp('.h5py', 'test')
os.close(fd)
h5save(fn, sel)
sel2 = h5load(fn)
os.remove(fn)
assert_equal(sel, sel2)
else:
sel2 = sel
# check that mask is OK even after I/O
assert_array_equal(sel.get_mask(), sel2.get_mask())
# test I/O with surfaces
# XXX the @tempfile decorator only supports a single filename
# hence this method does not use it
fd, outerfn = tempfile.mkstemp('outer.asc', 'test')
os.close(fd)
fd, innerfn = tempfile.mkstemp('inner.asc', 'test')
os.close(fd)
fd, volfn = tempfile.mkstemp('vol.nii', 'test')
os.close(fd)
surf.write(outerfn, outer, overwrite=True)
surf.write(innerfn, inner, overwrite=True)
img = sel.volgeom.get_empty_nifti_image()
img.to_filename(volfn)
sel3 = surf_voxel_selection.run_voxel_selection(
radius,
volfn,
innerfn,
outerfn,
source_surf_nodes=srcs,
distance_metric=distance_metric)
outer4 = surf.read(outerfn)
inner4 = surf.read(innerfn)
vsm4 = vs = volsurf.VolSurfMaximalMapping(vg, inner4, outer4)
# check that two ways of voxel selection match
sel4 = surf_voxel_selection.voxel_selection(
vsm4,
radius,
source_surf_nodes=srcs,
distance_metric=distance_metric)
assert_equal(sel3, sel4)
os.remove(outerfn)
os.remove(innerfn)
os.remove(volfn)
# compare sel3 with other selection results
# NOTE: which voxels are precisely selected by sel can be quite
# off from those in sel3, as writing the surfaces imposes
# rounding errors and the sphere is very symmetric, which
# means that different neighboring nodes are selected
# to select a certain number of voxels.
sel3cmp_difference_ratio = [(sel, .2), (sel4, 0.)]
for selcmp, ratio in sel3cmp_difference_ratio:
nunion = ndiff = 0
for k in selcmp.keys():
p = set(sel3.get(k))
q = set(selcmp.get(k))
nunion += len(p.union(q))
ndiff += len(p.symmetric_difference(q))
assert_true(float(ndiff) / float(nunion) <= ratio)
# check searchlight call
# as of late Aug 2012, this is with the fancy query engine
# as implemented by Yarik
mask = sel.get_mask()
keys = None if ncenters is None else sel.keys()
dset_data = np.reshape(np.arange(vg.nvoxels), vg.shape)
dset_img = nb.Nifti1Image(dset_data, vg.affine)
dset = fmri_dataset(samples=dset_img, mask=mask)
qe = queryengine.SurfaceVerticesQueryEngine(
sel,
# you can optionally add additional
# information about each near-disk-voxels
add_fa=['center_distances', 'grey_matter_position'])
# test i/o ensuring that when loading it is still trained
if externals.exists('h5py'):
fd, qefn = tempfile.mkstemp('qe.hdf5', 'test')
os.close(fd)
h5save(qefn, qe)
qe = h5load(qefn)
os.remove(qefn)
assert_false('ERROR' in repr(qe)) # to check if repr works
voxelcounter = _Voxel_Count_Measure()
searchlight = Searchlight(
voxelcounter,
queryengine=qe,
roi_ids=keys,
nproc=1,
enable_ca=['roi_feature_ids', 'roi_center_ids'])
sl_dset = searchlight(dset)
selected_count = sl_dset.samples[0, :]
mp = sel
for i, k in enumerate(sel.keys()):
# check that number of selected voxels matches
assert_equal(selected_count[i], len(mp[k]))
assert_equal(searchlight.ca.roi_center_ids, sel.keys())
assert_array_equal(sl_dset.fa['center_ids'], qe.ids)
# check nearest node is *really* the nearest node
allvx = sel.get_targets()
intermediate = outer * .5 + inner * .5
for vx in allvx:
nearest = sel.target2nearest_source(vx)
xyz = intermediate.vertices[nearest, :]
sqsum = np.sum((xyz - intermediate.vertices)**2, 1)
idx = np.argmin(sqsum)
assert_equal(idx, nearest)
if not tested_double_features: # test only once
# see if we have multiple features for the same voxel, we would get them all
dset1 = dset.copy()
dset1.fa['dset'] = [1]
dset2 = dset.copy()
dset2.fa['dset'] = [2]
dset_ = hstack((dset1, dset2), 'drop_nonunique')
dset_.sa = dset1.sa
# dset_.a.imghdr = dset1.a.imghdr
assert_true('imghdr' in dset_.a.keys())
assert_equal(dset_.a['imghdr'].value,
dset1.a['imghdr'].value)
roi_feature_ids = searchlight.ca.roi_feature_ids
sl_dset_ = searchlight(dset_)
# and we should get twice the counts
assert_array_equal(sl_dset_.samples, sl_dset.samples * 2)
# compare old and new roi_feature_ids
assert (len(roi_feature_ids) == len(
searchlight.ca.roi_feature_ids))
nfeatures = dset.nfeatures
for old, new in zip(roi_feature_ids,
searchlight.ca.roi_feature_ids):
# each new ids should comprise of old ones + (old + nfeatures)
# since we hstack'ed two datasets
assert_array_equal(
np.hstack([(x, x + nfeatures) for x in old]), new)
tested_double_features = True
# check whether number of voxels were selected is as expected
expected_voxcount = [22, 93, 183, 183, 183, 183, 183, 183, 183]
assert_equal(voxcount, expected_voxcount)
def test_surf(self, temp_fn):
"""Some simple testing with surfaces
"""
s = surf.generate_sphere(10)
assert_true(s.nvertices == 102)
assert_true(s.nfaces == 200)
v = s.vertices
f = s.faces
assert_true(v.shape == (102, 3))
assert_true(f.shape == (200, 3))
# another surface
t = s * 10 + 2
assert_true(t.same_topology(s))
assert_array_equal(f, t.faces)
assert_array_equal(v * 10 + 2, t.vertices)
# allow updating, but should not affect original array
# CHECKME: maybe we want to throw an exception instead
assert_true((v * 10 + 2 == t.vertices).all().all())
assert_true((s.vertices * 10 + 2 == t.vertices).all().all())
# a few checks on vertices and nodes
v_check = {
40: (0.86511144, -0.28109175, -0.41541501),
10: (0.08706015, -0.26794358, -0.95949297)
}
f_check = {10: (7, 8, 1), 40: (30, 31, 21)}
vf_checks = [(v_check, lambda x: x.vertices),
(f_check, lambda x: x.faces)]
eps = .0001
for cmap, f in vf_checks:
for k, v in cmap.iteritems():
surfval = f(s)[k, :]
assert_true((abs(surfval - v) < eps).all())
# make sure same topology fails with different topology
u = surf.generate_cube()
assert_false(u.same_topology(s))
# check that neighbours are computed correctly
# even if we nuke the topology afterwards
for _ in [0, 1]:
nbrs = s.neighbors
n_check = [(0, 96, 0.284629), (40, 39, 0.56218349),
(100, 99, 0.1741202)]
for i, j, k in n_check:
assert_true(abs(nbrs[i][j] - k) < eps)
def assign_zero(x):
x.faces[:, :] = 0
return None
assert_raises((ValueError, RuntimeError), assign_zero, s)
# see if mapping to high res works
h = surf.generate_sphere(40)
low2high = s.map_to_high_resolution_surf(h, .1)
partmap = {7: 141, 8: 144, 9: 148, 10: 153, 11: 157, 12: 281}
for k, v in partmap.iteritems():
assert_true(low2high[k] == v)
# ensure that slow implementation gives same results as fast one
low2high_slow = s.map_to_high_resolution_surf(h, .1)
for k, v in low2high.iteritems():
assert_true(low2high_slow[k] == v)
# should fail if epsilon is too small
assert_raises(ValueError,
lambda x: x.map_to_high_resolution_surf(h, .01), s)
n2f = s.node2faces
for i in xrange(s.nvertices):
nf = [10] if i < 2 else [5, 6] # number of faces expected
assert_true(len(n2f[i]) in nf)
# test dijkstra distances
ds2 = s.dijkstra_distance(2)
some_ds = {
0: 3.613173280799,
1: 0.2846296765,
2: 0.,
52: 1.87458018,
53: 2.0487004817,
54: 2.222820777,
99: 3.32854360,
100: 3.328543604,
101: 3.3285436042
}
eps = np.finfo('f').eps
for k, v in some_ds.iteritems():
assert_true(abs(v - ds2[k]) < eps)
# test I/O (through ascii files)
surf.write(temp_fn, s, overwrite=True)
s2 = surf.read(temp_fn)
# test i/o and ensure that the loaded instance is trained
if externals.exists('h5py'):
h5save(temp_fn, s2)
s2 = h5load(temp_fn)
assert_array_almost_equal(s.vertices, s2.vertices, 4)
assert_array_almost_equal(s.faces, s2.faces, 4)
# test plane (new feature end of August 2012)
s3 = surf.generate_plane((0, 0, 0), (2, 0, 0), (0, 1, 0), 10, 20)
assert_equal(s3.nvertices, 200)
assert_equal(s3.nfaces, 342)
assert_array_almost_equal(s3.vertices[-1, :], np.array([18., 19, 0.]))
assert_array_almost_equal(s3.faces[-1, :], np.array([199, 198, 179]))
# test bar
p, q = (0, 0, 0), (100, 0, 0)
s4 = surf.generate_bar(p, q, 10, 12)
assert_equal(s4.nvertices, 26)
assert_equal(s4.nfaces, 48)
def test_volume_mask_dict(self):
# also tests the outside_node_margin feature
sh = (10, 10, 10)
msk = np.zeros(sh)
for i in xrange(0, sh[0], 2):
msk[i, :, :] = 1
vol_affine = np.identity(4)
vol_affine[0, 0] = vol_affine[1, 1] = vol_affine[2, 2] = 2
vg = volgeom.VolGeom(sh, vol_affine, mask=msk)
density = 10
outer = surf.generate_sphere(density) * 10. + 5
inner = surf.generate_sphere(density) * 5. + 5
intermediate = outer * .5 + inner * .5
xyz = intermediate.vertices
radius = 50
outside_node_margins = [None, 0, 100., np.inf, True]
expected_center_count = [87] * 2 + [intermediate.nvertices] * 3
for k, outside_node_margin in enumerate(outside_node_margins):
sel = surf_voxel_selection.run_voxel_selection(
radius,
vg,
inner,
outer,
outside_node_margin=outside_node_margin)
assert_equal(intermediate, sel.source)
assert_equal(len(sel.keys()), expected_center_count[k])
assert_true(
set(sel.aux_keys()).issubset(
set(['center_distances', 'grey_matter_position'])))
msk_lin = msk.ravel()
sel_msk_lin = sel.get_mask().ravel()
for i in xrange(vg.nvoxels):
if msk_lin[i]:
src = sel.target2nearest_source(i)
assert_false((src is None) ^ (sel_msk_lin[i] == 0))
if src is None:
continue
# index of node nearest to voxel i
src_anywhere = sel.target2nearest_source(
i, fallback_euclidean_distance=True)
# coordinates of node nearest to voxel i
xyz_src = xyz[src_anywhere]
# coordinates of voxel i
xyz_trg = vg.lin2xyz(np.asarray([i]))
# distance between node nearest to voxel i, and voxel i
# this should be the smallest distancer
d = volgeom.distance(np.reshape(xyz_src, (1, 3)), xyz_trg)
# distances between all nodes and voxel i
ds = volgeom.distance(xyz, xyz_trg)
# order of the distances
is_ds = np.argsort(ds.ravel())
# go over all the nodes
# require that the node is in the volume
# mask
# index of node nearest to voxel i
ii = np.argmin(ds)
xyz_min = xyz[ii]
lin_min = vg.xyz2lin([xyz_min])
# linear index of voxel that contains xyz_src
lin_src = vg.xyz2lin(np.reshape(xyz_src, (1, 3)))
# when using multi-core support,
# pickling and unpickling can reduce the precision
# a little bit, causing rounding errors
eps = 1e-14
delta = np.abs(ds[ii] - d)
assert_false(delta > eps and ii in sel and i in sel[ii]
and vg.contains_lin(lin_min))
def test_mask_with_keys(self):
vol_shape = (10, 10, 10, 3)
vol_affine = np.identity(4)
vg = volgeom.VolGeom(vol_shape, vol_affine)
data = np.random.normal(size=vol_shape)
msk = np.ones(vol_shape[:3])
msk[:, 1:-1:2, :] = 0
ni_data = nb.Nifti1Image(data, vol_affine)
ni_msk = nb.Nifti1Image(msk, vol_affine)
ds = fmri_dataset(ni_data, mask=ni_msk)
sphere_density = 20
outer = surf.generate_sphere(sphere_density) * 10. + 5
inner = surf.generate_sphere(sphere_density) * 7. + 5
radius = 10
sel = surf_voxel_selection.run_voxel_selection(radius, ds,
inner, outer)
# in the mapping below:
# (tup: None) means that tup as input should raise a KeyError
# (tup: i) with i an int means that tup as input should return i
# elements
qe_ids2nvoxels = {SurfaceVoxelsQueryEngine:
{(1, 2, 3): 13,
tuple(np.arange(0, 200, 2)): 82,
(601,): None,
None: 126},
SurfaceVerticesQueryEngine:
{(1, 2, 3): None,
(205, 209, 210, 214): 36,
None: 126}}
for constructor, ids2nfeatures in qe_ids2nvoxels.iteritems():
qe = constructor(sel)
qe.train(ds)
img = qe.get_masked_nifti_image()
assert_array_equal(img.get_data(),
qe.get_masked_nifti_image(qe.ids).get_data())
img_getter = qe.get_masked_nifti_image
for ids, nfeatures in ids2nfeatures.iteritems():
ids_list = ids if ids is None else list(ids)
if nfeatures is None and ids is not None:
assert_raises(KeyError, img_getter, ids_list)
else:
img = img_getter(ids_list)
nfeatures_found = np.sum(img.get_data())
assert_equal(nfeatures, nfeatures_found)
if constructor is SurfaceVerticesQueryEngine:
expected_image = qe.get_masked_nifti_image(ids_list)
expected_mask = expected_image.get_data()
check_mask_func = lambda x: assert_array_equal(
expected_mask, x)
check_image_func = lambda x: check_mask_func(
x.get_data()) and \
assert_array_equal(x.affine,
expected_image.affine)
check_mask_func(sel.get_mask(ids_list))
check_image_func(sel.get_nifti_image_mask(ids_list))
tups = sel.get_voxel_indices(ids_list)
tups_mask = np.zeros(expected_mask.shape)
for tup in tups:
tups_mask[tup] += 1
assert_array_equal(expected_mask != 0, tups_mask != 0)
def test_voxel_selection_alternative_calls(self):
# Tests a multitude of different searchlight calls
# that all should yield exactly the same results.
#
# Calls differ by whether the arguments are filenames
# or data objects, whether values are specified explicityly
# or set to the default implicitly (using None).
# and by different calls to run the voxel selection.
#
# This method does not test for mask functionality.
# define the volume
vol_shape = (10, 10, 10, 3)
vol_affine = np.identity(4)
vol_affine[0, 0] = vol_affine[1, 1] = vol_affine[2, 2] = 5
# four versions: array, nifti image, file name, fmri dataset
volarr = np.ones(vol_shape)
volimg = nb.Nifti1Image(volarr, vol_affine)
# There is a detected problem with elderly NumPy's (e.g. 1.6.1
# on precise on travis) leading to segfaults while operating
# on memmapped volumes being forwarded to pprocess.
# Thus just making it compressed volume for those cases
suf = ".gz" if (externals.exists("pprocess") and externals.versions["numpy"] < "1.6.2") else ""
fd, volfn = tempfile.mkstemp("vol.nii" + suf, "test")
os.close(fd)
volimg.to_filename(volfn)
volds = fmri_dataset(volfn)
fd, volfngz = tempfile.mkstemp("vol.nii.gz", "test")
os.close(fd)
volimg.to_filename(volfngz)
voldsgz = fmri_dataset(volfngz)
# make the surfaces
sphere_density = 10
# two versions: Surface and file name
outer = surf.generate_sphere(sphere_density) * 25.0 + 15
inner = surf.generate_sphere(sphere_density) * 20.0 + 15
intermediate = inner * 0.5 + outer * 0.5
nv = outer.nvertices
fd, outerfn = tempfile.mkstemp("outer.asc", "test")
os.close(fd)
fd, innerfn = tempfile.mkstemp("inner.asc", "test")
os.close(fd)
fd, intermediatefn = tempfile.mkstemp("intermediate.asc", "test")
os.close(fd)
for s, fn in zip([outer, inner, intermediate], [outerfn, innerfn, intermediatefn]):
surf.write(fn, s, overwrite=True)
# searchlight radius (in mm)
radius = 10.0
# dataset used to run searchlight on
ds = fmri_dataset(volfn)
# simple voxel counter (run for each searchlight position)
m = _Voxel_Count_Measure()
# number of voxels expected in each searchlight
r_expected = np.array(
[
[
18,
9,
10,
9,
9,
9,
9,
10,
9,
9,
9,
9,
11,
11,
11,
11,
10,
10,
10,
9,
10,
11,
9,
10,
10,
8,
7,
8,
8,
8,
9,
10,
12,
12,
11,
7,
7,
8,
5,
9,
11,
11,
12,
12,
9,
5,
8,
7,
7,
12,
12,
13,
12,
12,
7,
7,
8,
5,
9,
12,
12,
13,
11,
9,
5,
8,
7,
7,
11,
12,
12,
11,
12,
10,
10,
11,
9,
11,
12,
12,
12,
12,
16,
13,
16,
16,
16,
17,
15,
17,
17,
17,
16,
16,
16,
18,
16,
16,
16,
16,
18,
16,
]
]
)
params = dict(
intermediate_=(intermediate, intermediatefn, None),
center_nodes_=(None, range(nv)),
volume_=(volimg, volfn, volds, volfngz, voldsgz),
surf_src_=("filename", "surf"),
volume_mask_=(None, True, 0, 2),
call_method_=("qe", "rvs", "gam"),
)
combis = _cartprod(params) # compute all possible combinations
combistep = 17 # 173
# some fine prime number to speed things up
# if this value becomes too big then not all
# cases are covered
# the unit test tests itself whether all values
# occur at least once
tested_params = dict()
def val2str(x):
return "%r:%r" % (type(x), x)
for i in xrange(0, len(combis), combistep):
combi = combis[i]
intermediate_ = combi["intermediate_"]
center_nodes_ = combi["center_nodes_"]
volume_ = combi["volume_"]
surf_src_ = combi["surf_src_"]
volume_mask_ = combi["volume_mask_"]
call_method_ = combi["call_method_"]
# keep track of which values were used -
# so that this unit test tests itself
for k in combi.keys():
if not k in tested_params:
tested_params[k] = set()
tested_params[k].add(val2str(combi[k]))
if surf_src_ == "filename":
s_i, s_m, s_o = inner, intermediate, outer
elif surf_src_ == "surf":
s_i, s_m, s_o = innerfn, intermediatefn, outerfn
else:
raise ValueError("this should not happen")
if call_method_ == "qe":
# use the fancy query engine wrapper
qe = disc_surface_queryengine(
radius, volume_, s_i, s_o, s_m, source_surf_nodes=center_nodes_, volume_mask=volume_mask_
)
sl = Searchlight(m, queryengine=qe)
r = sl(ds).samples
elif call_method_ == "rvs":
# use query-engine but build the
# ingredients by hand
vg = volgeom.from_any(volume_, volume_mask_)
vs = volsurf.VolSurfMaximalMapping(vg, s_i, s_o)
sel = surf_voxel_selection.voxel_selection(vs, radius, source_surf=s_m, source_surf_nodes=center_nodes_)
qe = SurfaceVerticesQueryEngine(sel)
sl = Searchlight(m, queryengine=qe)
r = sl(ds).samples
elif call_method_ == "gam":
# build everything from the ground up
vg = volgeom.from_any(volume_, volume_mask_)
vs = volsurf.VolSurfMaximalMapping(vg, s_i, s_o)
sel = surf_voxel_selection.voxel_selection(vs, radius, source_surf=s_m, source_surf_nodes=center_nodes_)
mp = sel
ks = sel.keys()
nk = len(ks)
r = np.zeros((1, nk))
for i, k in enumerate(ks):
r[0, i] = len(mp[k])
# check if result is as expected
assert_array_equal(r_expected, r)
# clean up
all_fns = [volfn, volfngz, outerfn, innerfn, intermediatefn]
map(os.remove, all_fns)
for k, vs in params.iteritems():
if not k in tested_params:
raise ValueError("Missing key: %r" % k)
for v in vs:
vstr = val2str(v)
if not vstr in tested_params[k]:
raise ValueError("Missing value %r for %s" % (tested_params[k], k))
def test_surf_voxel_selection(self):
vol_shape = (10, 10, 10)
vol_affine = np.identity(4)
vol_affine[0, 0] = vol_affine[1, 1] = vol_affine[2, 2] = 5
vg = volgeom.VolGeom(vol_shape, vol_affine)
density = 10
outer = surf.generate_sphere(density) * 25. + 15
inner = surf.generate_sphere(density) * 20. + 15
vs = volsurf.VolSurfMaximalMapping(vg, outer, inner)
nv = outer.nvertices
# select under variety of parameters
# parameters are distance metric (dijkstra or euclidean),
# radius, and number of searchlight centers
params = [('d', 1., 10), ('d', 1., 50), ('d', 1., 100), ('d', 2., 100),
('e', 2., 100), ('d', 2., 100), ('d', 20, 100),
('euclidean', 5, None), ('dijkstra', 10, None)]
# function that indicates for which parameters the full test is run
test_full = lambda x:len(x[0]) > 1 or x[2] == 100
expected_labs = ['grey_matter_position',
'center_distances']
voxcount = []
tested_double_features = False
for param in params:
distance_metric, radius, ncenters = param
srcs = range(0, nv, nv // (ncenters or nv))
sel = surf_voxel_selection.voxel_selection(vs, radius,
source_surf_nodes=srcs,
distance_metric=distance_metric)
# see how many voxels were selected
vg = sel.volgeom
datalin = np.zeros((vg.nvoxels, 1))
mp = sel
for k, idxs in mp.iteritems():
if idxs is not None:
datalin[idxs] = 1
voxcount.append(np.sum(datalin))
if test_full(param):
assert_equal(np.sum(datalin), np.sum(sel.get_mask()))
assert_true(len('%s%r' % (sel, sel)) > 0)
# see if voxels containing inner and outer
# nodes were selected
for sf in [inner, outer]:
for k, idxs in mp.iteritems():
xyz = np.reshape(sf.vertices[k, :], (1, 3))
linidx = vg.xyz2lin(xyz)
# only required if xyz is actually within the volume
assert_equal(linidx in idxs, vg.contains_lin(linidx))
# check that it has all the attributes
labs = sel.aux_keys()
assert_true(all([lab in labs for lab in expected_labs]))
if externals.exists('h5py'):
# some I/O testing
fd, fn = tempfile.mkstemp('.h5py', 'test'); os.close(fd)
h5save(fn, sel)
sel2 = h5load(fn)
os.remove(fn)
assert_equal(sel, sel2)
else:
sel2 = sel
# check that mask is OK even after I/O
assert_array_equal(sel.get_mask(), sel2.get_mask())
# test I/O with surfaces
# XXX the @tempfile decorator only supports a single filename
# hence this method does not use it
fd, outerfn = tempfile.mkstemp('outer.asc', 'test'); os.close(fd)
fd, innerfn = tempfile.mkstemp('inner.asc', 'test'); os.close(fd)
fd, volfn = tempfile.mkstemp('vol.nii', 'test'); os.close(fd)
surf.write(outerfn, outer, overwrite=True)
surf.write(innerfn, inner, overwrite=True)
img = sel.volgeom.get_empty_nifti_image()
img.to_filename(volfn)
sel3 = surf_voxel_selection.run_voxel_selection(radius, volfn, innerfn,
outerfn, source_surf_nodes=srcs,
distance_metric=distance_metric)
outer4 = surf.read(outerfn)
inner4 = surf.read(innerfn)
vsm4 = vs = volsurf.VolSurfMaximalMapping(vg, inner4, outer4)
# check that two ways of voxel selection match
sel4 = surf_voxel_selection.voxel_selection(vsm4, radius,
source_surf_nodes=srcs,
distance_metric=distance_metric)
assert_equal(sel3, sel4)
os.remove(outerfn)
os.remove(innerfn)
os.remove(volfn)
# compare sel3 with other selection results
# NOTE: which voxels are precisely selected by sel can be quite
# off from those in sel3, as writing the surfaces imposes
# rounding errors and the sphere is very symmetric, which
# means that different neighboring nodes are selected
# to select a certain number of voxels.
sel3cmp_difference_ratio = [(sel, .2), (sel4, 0.)]
for selcmp, ratio in sel3cmp_difference_ratio:
nunion = ndiff = 0
for k in selcmp.keys():
p = set(sel3.get(k))
q = set(selcmp.get(k))
nunion += len(p.union(q))
ndiff += len(p.symmetric_difference(q))
assert_true(float(ndiff) / float(nunion) <= ratio)
# check searchlight call
# as of late Aug 2012, this is with the fancy query engine
# as implemented by Yarik
mask = sel.get_mask()
keys = None if ncenters is None else sel.keys()
dset_data = np.reshape(np.arange(vg.nvoxels), vg.shape)
dset_img = nb.Nifti1Image(dset_data, vg.affine)
dset = fmri_dataset(samples=dset_img, mask=mask)
qe = queryengine.SurfaceVerticesQueryEngine(sel,
# you can optionally add additional
# information about each near-disk-voxels
add_fa=['center_distances',
'grey_matter_position'])
# test i/o ensuring that when loading it is still trained
if externals.exists('h5py'):
fd, qefn = tempfile.mkstemp('qe.hdf5', 'test'); os.close(fd)
h5save(qefn, qe)
qe = h5load(qefn)
os.remove(qefn)
assert_false('ERROR' in repr(qe)) # to check if repr works
voxelcounter = _Voxel_Count_Measure()
searchlight = Searchlight(voxelcounter, queryengine=qe, roi_ids=keys, nproc=1,
enable_ca=['roi_feature_ids', 'roi_center_ids'])
sl_dset = searchlight(dset)
selected_count = sl_dset.samples[0, :]
mp = sel
for i, k in enumerate(sel.keys()):
# check that number of selected voxels matches
assert_equal(selected_count[i], len(mp[k]))
assert_equal(searchlight.ca.roi_center_ids, sel.keys())
assert_array_equal(sl_dset.fa['center_ids'], qe.ids)
# check nearest node is *really* the nearest node
allvx = sel.get_targets()
intermediate = outer * .5 + inner * .5
for vx in allvx:
nearest = sel.target2nearest_source(vx)
xyz = intermediate.vertices[nearest, :]
sqsum = np.sum((xyz - intermediate.vertices) ** 2, 1)
idx = np.argmin(sqsum)
assert_equal(idx, nearest)
if not tested_double_features: # test only once
# see if we have multiple features for the same voxel, we would get them all
dset1 = dset.copy()
dset1.fa['dset'] = [1]
dset2 = dset.copy()
dset2.fa['dset'] = [2]
dset_ = hstack((dset1, dset2), 'drop_nonunique')
dset_.sa = dset1.sa
#dset_.a.imghdr = dset1.a.imghdr
assert_true('imghdr' in dset_.a.keys())
assert_equal(dset_.a['imghdr'].value, dset1.a['imghdr'].value)
roi_feature_ids = searchlight.ca.roi_feature_ids
sl_dset_ = searchlight(dset_)
# and we should get twice the counts
assert_array_equal(sl_dset_.samples, sl_dset.samples * 2)
# compare old and new roi_feature_ids
assert(len(roi_feature_ids) == len(searchlight.ca.roi_feature_ids))
nfeatures = dset.nfeatures
for old, new in zip(roi_feature_ids,
searchlight.ca.roi_feature_ids):
# each new ids should comprise of old ones + (old + nfeatures)
# since we hstack'ed two datasets
assert_array_equal(np.hstack([(x, x + nfeatures) for x in old]),
new)
tested_double_features = True
# check whether number of voxels were selected is as expected
expected_voxcount = [22, 93, 183, 183, 183, 183, 183, 183, 183]
assert_equal(voxcount, expected_voxcount)
def test_surf(self, temp_fn):
"""Some simple testing with surfaces
"""
s = surf.generate_sphere(10)
assert_true(s.nvertices == 102)
assert_true(s.nfaces == 200)
v = s.vertices
f = s.faces
assert_true(v.shape == (102, 3))
assert_true(f.shape == (200, 3))
# another surface
t = s * 10 + 2
assert_true(t.same_topology(s))
assert_array_equal(f, t.faces)
assert_array_equal(v * 10 + 2, t.vertices)
# allow updating, but should not affect original array
# CHECKME: maybe we want to throw an exception instead
assert_true((v * 10 + 2 == t.vertices).all().all())
assert_true((s.vertices * 10 + 2 == t.vertices).all().all())
# a few checks on vertices and nodes
v_check = {40:(0.86511144 , -0.28109175, -0.41541501),
10:(0.08706015, -0.26794358, -0.95949297)}
f_check = {10:(7, 8, 1), 40:(30, 31, 21)}
vf_checks = [(v_check, lambda x:x.vertices),
(f_check, lambda x:x.faces)]
eps = .0001
for cmap, f in vf_checks:
for k, v in cmap.iteritems():
surfval = f(s)[k, :]
assert_true((abs(surfval - v) < eps).all())
# make sure same topology fails with different topology
u = surf.generate_cube()
assert_false(u.same_topology(s))
# check that neighbours are computed correctly
# even if we nuke the topology afterwards
for _ in [0, 1]:
nbrs = s.neighbors
n_check = [(0, 96, 0.284629),
(40, 39, 0.56218349),
(100, 99, 0.1741202)]
for i, j, k in n_check:
assert_true(abs(nbrs[i][j] - k) < eps)
def assign_zero(x):
x.faces[:, :] = 0
return None
assert_raises((ValueError, RuntimeError), assign_zero, s)
# see if mapping to high res works
h = surf.generate_sphere(40)
low2high = s.map_to_high_resolution_surf(h, .1)
partmap = {7: 141, 8: 144, 9: 148, 10: 153, 11: 157, 12: 281}
for k, v in partmap.iteritems():
assert_true(low2high[k] == v)
# ensure that slow implementation gives same results as fast one
low2high_slow = s.map_to_high_resolution_surf(h, .1)
for k, v in low2high.iteritems():
assert_true(low2high_slow[k] == v)
# should fail if epsilon is too small
assert_raises(ValueError,
lambda x:x.map_to_high_resolution_surf(h, .01), s)
n2f = s.node2faces
for i in xrange(s.nvertices):
nf = [10] if i < 2 else [5, 6] # number of faces expected
assert_true(len(n2f[i]) in nf)
# test dijkstra distances
ds2 = s.dijkstra_distance(2)
some_ds = {0: 3.613173280799, 1: 0.2846296765, 2: 0.,
52: 1.87458018, 53: 2.0487004817, 54: 2.222820777,
99: 3.32854360, 100: 3.328543604, 101: 3.3285436042}
eps = np.finfo('f').eps
for k, v in some_ds.iteritems():
assert_true(abs(v - ds2[k]) < eps)
# test I/O (through ascii files)
surf.write(temp_fn, s, overwrite=True)
s2 = surf.read(temp_fn)
# test i/o and ensure that the loaded instance is trained
if externals.exists('h5py'):
h5save(temp_fn, s2)
s2 = h5load(temp_fn)
assert_array_almost_equal(s.vertices, s2.vertices, 4)
assert_array_almost_equal(s.faces, s2.faces, 4)
# test plane (new feature end of August 2012)
s3 = surf.generate_plane((0, 0, 0), (2, 0, 0), (0, 1, 0), 10, 20)
assert_equal(s3.nvertices, 200)
assert_equal(s3.nfaces, 342)
assert_array_almost_equal(s3.vertices[-1, :], np.array([18., 19, 0.]))
assert_array_almost_equal(s3.faces[-1, :], np.array([199, 198, 179]))
# test bar
p, q = (0, 0, 0), (100, 0, 0)
s4 = surf.generate_bar(p, q, 10, 12)
assert_equal(s4.nvertices, 26)
assert_equal(s4.nfaces, 48)
def test_volume_mask_dict(self):
# also tests the outside_node_margin feature
sh = (10, 10, 10)
msk = np.zeros(sh)
for i in xrange(0, sh[0], 2):
msk[i, :, :] = 1
vol_affine = np.identity(4)
vol_affine[0, 0] = vol_affine[1, 1] = vol_affine[2, 2] = 2
vg = volgeom.VolGeom(sh, vol_affine, mask=msk)
density = 10
outer = surf.generate_sphere(density) * 10. + 5
inner = surf.generate_sphere(density) * 5. + 5
intermediate = outer * .5 + inner * .5
xyz = intermediate.vertices
radius = 50
outside_node_margins = [None, 0, 100., np.inf, True]
expected_center_count = [87] * 2 + [intermediate.nvertices] * 3
for k, outside_node_margin in enumerate(outside_node_margins):
sel = surf_voxel_selection.run_voxel_selection(radius, vg, inner,
outer, outside_node_margin=outside_node_margin)
assert_equal(intermediate, sel.source)
assert_equal(len(sel.keys()), expected_center_count[k])
assert_true(set(sel.aux_keys()).issubset(set(['center_distances',
'grey_matter_position'])))
msk_lin = msk.ravel()
sel_msk_lin = sel.get_mask().ravel()
for i in xrange(vg.nvoxels):
if msk_lin[i]:
src = sel.target2nearest_source(i)
assert_false((src is None) ^ (sel_msk_lin[i] == 0))
if src is None:
continue
# index of node nearest to voxel i
src_anywhere = sel.target2nearest_source(i,
fallback_euclidean_distance=True)
# coordinates of node nearest to voxel i
xyz_src = xyz[src_anywhere]
# coordinates of voxel i
xyz_trg = vg.lin2xyz(np.asarray([i]))
# distance between node nearest to voxel i, and voxel i
# this should be the smallest distancer
d = volgeom.distance(np.reshape(xyz_src, (1, 3)), xyz_trg)
# distances between all nodes and voxel i
ds = volgeom.distance(xyz, xyz_trg)
# order of the distances
is_ds = np.argsort(ds.ravel())
# go over all the nodes
# require that the node is in the volume
# mask
# index of node nearest to voxel i
ii = np.argmin(ds)
xyz_min = xyz[ii]
lin_min = vg.xyz2lin([xyz_min])
# linear index of voxel that contains xyz_src
lin_src = vg.xyz2lin(np.reshape(xyz_src, (1, 3)))
# when using multi-core support,
# pickling and unpickling can reduce the precision
# a little bit, causing rounding errors
eps = 1e-14
delta = np.abs(ds[ii] - d)
assert_false(delta > eps and ii in sel and
i in sel[ii] and
vg.contains_lin(lin_min))
def test_voxel_selection_alternative_calls(self):
# Tests a multitude of different searchlight calls
# that all should yield exactly the same results.
#
# Calls differ by whether the arguments are filenames
# or data objects, whether values are specified explicityly
# or set to the default implicitly (using None).
# and by different calls to run the voxel selection.
#
# This method does not test for mask functionality.
# define the volume
vol_shape = (10, 10, 10, 3)
vol_affine = np.identity(4)
vol_affine[0, 0] = vol_affine[1, 1] = vol_affine[2, 2] = 5
# four versions: array, nifti image, file name, fmri dataset
volarr = np.ones(vol_shape)
volimg = nb.Nifti1Image(volarr, vol_affine)
# There is a detected problem with elderly NumPy's (e.g. 1.6.1
# on precise on travis) leading to segfaults while operating
# on memmapped volumes being forwarded to pprocess.
# Thus just making it compressed volume for those cases
suf = '.gz' \
if externals.exists('pprocess') and externals.versions['numpy'] < '1.6.2' \
else ''
fd, volfn = tempfile.mkstemp('vol.nii' + suf, 'test')
os.close(fd)
volimg.to_filename(volfn)
volds = fmri_dataset(volfn)
fd, volfngz = tempfile.mkstemp('vol.nii.gz', 'test')
os.close(fd)
volimg.to_filename(volfngz)
voldsgz = fmri_dataset(volfngz)
# make the surfaces
sphere_density = 10
# two versions: Surface and file name
outer = surf.generate_sphere(sphere_density) * 25. + 15
inner = surf.generate_sphere(sphere_density) * 20. + 15
intermediate = inner * .5 + outer * .5
nv = outer.nvertices
fd, outerfn = tempfile.mkstemp('outer.asc', 'test')
os.close(fd)
fd, innerfn = tempfile.mkstemp('inner.asc', 'test')
os.close(fd)
fd, intermediatefn = tempfile.mkstemp('intermediate.asc', 'test')
os.close(fd)
for s, fn in zip([outer, inner, intermediate],
[outerfn, innerfn, intermediatefn]):
surf.write(fn, s, overwrite=True)
# searchlight radius (in mm)
radius = 10.
# dataset used to run searchlight on
ds = fmri_dataset(volfn)
# simple voxel counter (run for each searchlight position)
m = _Voxel_Count_Measure()
# number of voxels expected in each searchlight
r_expected = np.array([[
18, 9, 10, 9, 9, 9, 9, 10, 9, 9, 9, 9, 11, 11, 11, 11, 10, 10, 10,
9, 10, 11, 9, 10, 10, 8, 7, 8, 8, 8, 9, 10, 12, 12, 11, 7, 7, 8, 5,
9, 11, 11, 12, 12, 9, 5, 8, 7, 7, 12, 12, 13, 12, 12, 7, 7, 8, 5,
9, 12, 12, 13, 11, 9, 5, 8, 7, 7, 11, 12, 12, 11, 12, 10, 10, 11,
9, 11, 12, 12, 12, 12, 16, 13, 16, 16, 16, 17, 15, 17, 17, 17, 16,
16, 16, 18, 16, 16, 16, 16, 18, 16
]])
params = dict(intermediate_=(intermediate, intermediatefn, None),
center_nodes_=(None, range(nv)),
volume_=(volimg, volfn, volds, volfngz, voldsgz),
surf_src_=('filename', 'surf'),
volume_mask_=(None, True, 0, 2),
call_method_=("qe", "rvs", "gam"))
combis = _cartprod(params) # compute all possible combinations
combistep = 17 #173
# some fine prime number to speed things up
# if this value becomes too big then not all
# cases are covered
# the unit test tests itself whether all values
# occur at least once
tested_params = dict()
def val2str(x):
return '%r:%r' % (type(x), x)
for i in xrange(0, len(combis), combistep):
combi = combis[i]
intermediate_ = combi['intermediate_']
center_nodes_ = combi['center_nodes_']
volume_ = combi['volume_']
surf_src_ = combi['surf_src_']
volume_mask_ = combi['volume_mask_']
call_method_ = combi['call_method_']
# keep track of which values were used -
# so that this unit test tests itself
for k in combi.keys():
if not k in tested_params:
tested_params[k] = set()
tested_params[k].add(val2str(combi[k]))
if surf_src_ == 'filename':
s_i, s_m, s_o = inner, intermediate, outer
elif surf_src_ == 'surf':
s_i, s_m, s_o = innerfn, intermediatefn, outerfn
else:
raise ValueError('this should not happen')
if call_method_ == "qe":
# use the fancy query engine wrapper
qe = disc_surface_queryengine(radius,
volume_,
s_i,
s_o,
s_m,
source_surf_nodes=center_nodes_,
volume_mask=volume_mask_)
sl = Searchlight(m, queryengine=qe)
r = sl(ds).samples
elif call_method_ == 'rvs':
# use query-engine but build the
# ingredients by hand
vg = volgeom.from_any(volume_, volume_mask_)
vs = volsurf.VolSurfMaximalMapping(vg, s_i, s_o)
sel = surf_voxel_selection.voxel_selection(
vs,
radius,
source_surf=s_m,
source_surf_nodes=center_nodes_)
qe = SurfaceVerticesQueryEngine(sel)
sl = Searchlight(m, queryengine=qe)
r = sl(ds).samples
elif call_method_ == 'gam':
# build everything from the ground up
vg = volgeom.from_any(volume_, volume_mask_)
vs = volsurf.VolSurfMaximalMapping(vg, s_i, s_o)
sel = surf_voxel_selection.voxel_selection(
vs,
radius,
source_surf=s_m,
source_surf_nodes=center_nodes_)
mp = sel
ks = sel.keys()
nk = len(ks)
r = np.zeros((1, nk))
for i, k in enumerate(ks):
r[0, i] = len(mp[k])
# check if result is as expected
assert_array_equal(r_expected, r)
# clean up
all_fns = [volfn, volfngz, outerfn, innerfn, intermediatefn]
map(os.remove, all_fns)
for k, vs in params.iteritems():
if not k in tested_params:
raise ValueError("Missing key: %r" % k)
for v in vs:
vstr = val2str(v)
if not vstr in tested_params[k]:
raise ValueError("Missing value %r for %s" %
(tested_params[k], k))
